Fig. 6

Conserved sequence motifs in the J element. a Schematic illustration of putative binding motifs of the homeodomain site (TAATKR; blue arrowheads), an O/E-like site (YYYCARRRR; orange arrowheads), and a class I-specific conserved motif, the AAACTTTTC site (green arrowheads) in the J, H, and P elements in mice. The asterisks represent the extended homeodomain site (5′-AACTTTTTAATGA-3′). The orientation of the motifs on either DNA strand is represented by arrowheads pointing in different directions. The VISTA plot between mouse and human is shown at the top. The shaded box represents the core J element with highest homology; it contains multiple conserved motifs. b Multiple alignment of a 430-bp sequence, the core J element (shaded box in a), from eleven mammals, including placental and aplacental mammals. Comparison of the sequences reveals six stretches of homology, which are indicated by colored boxes: one AAACTTTTC sequence (green box), four potential homeodomain sites (blue), and one O/E-like site (orange box). The blue line depicts a stretch of additional sequence homology upstream of the homeodomain called the extended homeodomain-like site